Allocator is a graph neural network-based framework for mRNA subcellular localization prediction

Abstract

AbstractThe asymmetrical distribution of expressed mRNAs tightly controls the precise synthesis of proteins within human cells. This non-uniform distribution, a cornerstone of developmental biology, plays a pivotal role in numerous cellular processes. To advance our comprehension of gene regulatory networks, it is essential to develop computational tools for accurately identifying the subcellular localizations of mRNAs. However, considering multi-localization phenomena remains limited in existing approaches, with none considering the influence of RNA’s secondary structure. In this study, we introduce ‘Allocator’, a deep learning-based model that seamlessly integrates both sequence-level and structure-level information, significantly enhancing the prediction of mRNA multi-localization. The Allocator models equip four efficient feature extractors, each designed to handle different inputs. Two are tailored for sequence-based inputs, incorporating multilayer perceptron and multi-head self-attention mechanisms. The other two are specialized in processing structure-based inputs, employing graph neural networks. Benchmarking results underscore Allocator’s superiority over state-of-the-art methods, showcasing its strength in revealing intricate localization associations. Furthermore, we have developed a user-friendly web server for Allocator, enhancing its accessibility. You can explore Allocator through our web server, available athttp://Allocator.unimelb-biotools.cloud.edu.au.